High school student Daisuke Higashida reluctantly takes up a part-time job at Wagnaria after his father's company goes bankrupt. Daisuke begins training under floor chief Hana Miyakoshi, who is rather harsh towards dimwitted manager Kenichiro Sakaki, also meeting the other staff members; Sayuri Muranushi, who can see ghosts but refuses to believe in them. Kisaki Kondou, a former delinquent who rarely does any work, Shiho Kamakura, a rich girl who refers to customers as "the common masses" and uses her money to avoid having to apologize. Masahiro Adachi and Takuya Kouno, who both work in the kitchen, and Yuuta Shindou, who is frequently tormented by Kamakura as his father owes a large debt to her father

Miyakoshi asks Daisuke to tutor her as her mother is threatening to make her quit if she gets bad grades. Kisaki starts bringing her baby daughter, Hime, to work. Sakaki is punished by Miyakoshi after hiring Kouki Saiki, who can only speak English. Kisaki decides to train him, as only she can speak English.

Daisuke suspects a new customer, Miri Yanagiba, might be a ghost. Muranushi insists she is not, though she is the granddaughter of the old man who visits every day, who is definitely a ghost. Daisuke learns Yanagiba was supposed to attend his school but after missing her chance to make friends she became a truant. Daisuke plans to introduce her to Rui Nagata, a girl in his class, so she can be her friend.

Shindou becomes depressed after Kamakura torments him worse than usual. Kouno suspects Adachi is in love with Muranushi. Meanwhile Muranushi suspects Daisuke likes Miyakoshi since he acts differently around her. Miyakoshi refuses to believe her chocolate changed his personality. Her mother, Youko, visits Wagnaria, having mixed up the date of her husband’s birthday, revealing that while she pretends not to care, she misses him.

The staff notices that Daisuke's personality has gotten worse after Miyakoshi's latest chocolate disaster. Daisuke takes an interest in the manager, Sakaki, who is still employed despite his incompetence and appears to have a lot of spare money. One of Kamakura's bodyguards, Tasaka, who is actually employed to keep Kamakura from killing Shindou, reveals that Sakaki was a delinquent famous for fighting with his cat on his head.

Kamakura continues to torment Shindou. The financially savvy baby Hime gives Shindou lottery tickets she was playing with, only for Shindou to discover a ticket worth 300 million yen, enough to pay his entire debt.

With St. Valentine telling her love would improve her cooking Miyakoshi asks Daisuke to date her. Daisuke agrees, but only to prove what a bad match they are so she will break up with him. The news devastates Nagata but when Daisuke explains he is only dating Miyakoshi so she will break up with him Nagata scolds him for being a bad boyfriend.

Muranushi becomes ill and her absence upsets the old man’s ghost who visits her every day, causing him to begin haunting Wagnaria. Adachi feels guilty at upsetting Muranushi and causing her to become ill so he decides to visit her home and apologise again with shop sweets he got from Miyakoshi. After he sees how ill she is he insists they go to the doctor, though she refuses after getting upset at her mother.

Miyakoshi continues to enjoy herself with Daisuke always paying for dates but admits she sometimes feels guilty. Shindou remembers that his father had told him to marry Kamakura so his gambling debt would be cancelled. This caused him to turn down Kamakura’s offer of marriage on principle.

Muranushi and Kisaki try to tell Miyakoshi to consider Daisuke’s feelings. Daisuke asks why Miyakoshi never pays for dates and she admits she forgot her ATM number and relies on money from her mother. Miyakoshi announces she will be sleeping at Daisuke’s house, after which Daisuke learns his family will be absent meaning he and Miyakoshi will be “alone together”.

Everyone at Wagnaria begins acting strangely due to all the romantic problems. Kamakura worries Shindou may never pay his debt and lashes out at him. Adachi asks Muranushi on a date but suspects she is going to break up with him, though it turns out Muranushi thought he wanted to break up with her. She is relieved to learn he was confused over seeing Miyakoshi almost “give herself” to Daisuke and she smiles, though this time it doesn’t scare him.

Daisuke dismisses Miyakoshi’s worries about sex, assuring her they can continue trying to improve her cooking and nothing else. Miyakoshi becomes unexpectedly enthusiastic about cooking to make Daisuke happy but tries so hard her kitchen emits a disturbing miasma. Daisuke surprisingly orders her to make chocolate again, and while it is disgusting, he does not meet St. Valentine.